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Yorodumi- PDB-4jgf: Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jgf | ||||||
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Title | Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin Mutant | ||||||
Components | Gamma-crystallin D | ||||||
Keywords | STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information lens fiber cell differentiation / structural constituent of eye lens / lens development in camera-type eye / visual perception / cellular response to reactive oxygen species / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ji, F.L. / Koharudin, L.M. / Jung, J.W. / Gronenborn, A.M. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Crystal structure of the cataract-causing P23T gamma D-crystallin mutant. Authors: Ji, F. / Koharudin, L.M. / Jung, J. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jgf.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jgf.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jgf ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jgf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20404.705 Da / Num. of mol.: 2 / Fragment: HUMAN GAMMA D CRYSTALLIN MUTANT / Mutation: P23T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli (E. coli) / References: UniProt: P07320 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.17 M CH3COONH4, 0.085 M C2H3NaO2 3H2O, 25.5% (w/v) PEG 4000, and 15% (v/v) glycerol , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 4, 2012 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32.01 Å / Num. obs: 10719 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.533 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.826 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→32.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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